Genome engineering is a common term to summarize different techniques to insert, delete, substitute or otherwise manipulate specific genetic sequences within a genome and has numerous therapeutic and biotechnological applications. More or less all genome engineering techniques use recombinases, integrases or endonucleases to create DNA double strand breaks at predetermined sites in order to promote homologous recombination.
In spite of the fact that numerous methods have been employed to create DNA double strand breaks, the development of effective means to create DNA double strand breaks at highly specific sites in a genome remains a major goal in gene therapy, agrotechnology, and synthetic biology.
One approach to achieve this goal is to use nucleases with specificity for a sequence that is sufficiently large to be present at only a single site within a genome. Nucleases recognizing such large DNA sequences of about 15 to 30 nucleotides are therefore called “meganucleases” or “homing endonucleases” and are frequently associated with parasitic DNA elements, such as group 1 self-splicing introns and inteins commonly found in the genomes of plants and fungi. Meganucleases are commonly grouped into four families: the LAGLIDADG family, the GIY-YIG family, the His-Cys box family and the HNH family. These families are characterized by structural motifs, which affect catalytic activity and the sequence of their DNA recognition sequences. Natural meganucleases from the LAGLIDADG family have been used to effectively promote site-specific genome modifications in insect and mammalian cell cultures, as well as in many organisms, such as plants, yeast or mice, but this approach has been limited to the modification of either homologous genes that conserve the DNA recognition sequence or to preengineered genomes into which a recognition sequence has been introduced. In order to avoid these limitations and to promote the systematic implementation of DNA double strand break stimulated gene modification new types of nucleases have been created.
One type of new nucleases consists of artificial combinations of unspecific nucleases to a highly specific DNA binding domain. The effectiveness of this strategy has been demonstrated in a variety of organisms using chimeric fusions between an engineered zinc finger DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme (e.g. WO03/089452) a variation of this approach is to use an inactive variant of a meganuclease as DNA binding domain fused to an unspecific nuclease like FokI as disclosed in Lippow et al., “Creation of a type IIS restriction endonuclease with a long recognition sequence”, Nucleic Acid Research (2009), Vol. 37, No. 9, pages 3061 to 3073.
An alternative approach is to genetically engineer natural meganucleases in order to customize their DNA binding regions to bind existing sites in a genome, thereby creating engineered meganucleases having new specificities (e.g WO07093918, WO2008/093249, WO09114321).
However, many meganucleases which have been engineered with respect to DNA cleavage specificity have decreased cleavage activity relative to the naturally occurring meganucleases from which they are derived (US2010/0071083). Most meganucleases do also act on sequences similar to their optimal binding site, which may lead to unintended or even detrimental off-target effects. Despite the fact, that several approaches have already been taken to avoid enhance the efficiency of meganuclease induced homologous recombination e.g. by fusing nucleases to the ligand binding domain of the rat Glucocorticoid Receptor in order to promote or even induce the transport of this modified nuclease to the cell nucleus and therefore its target sites by the addition of dexamethasone or similar compounds (WO02007/135022), there is still a need in the art to develop meganucleases having high induction rates of homologous recombination and/or a high specificity in regard to their binding site, thereby limiting the risk of off-target effects.